Could some kind person tell me where would the official documentation by William 1V regarding the allowance of officers to sit (on ship only) and toast the King, be kept.
There must be some record somewhere as William would have had to get permission from King George 111, before he could pass this order.

You could try contacting the Royal Archives - they might be able to help.

The Royal Archives, Windsor Castle, Windsor, Berkshire SL4 1NJ.

However, it does state the following on their website:

The Royal Archives contains a number of collections of papers, mostly from the reign of King George III (1760-1820) onwards.

The official correspondence of King William IV was destroyed, virtually in its entirety, after his death by his surviving executor; however, some of the papers of his two Prime Ministers, Lords Grey and Melbourne, have been given to the Royal Archives. Only a small amount of random material has survived in the Royal Archives for the earlier Hanoverian Kings.